The phone call uses the regular microphone. When you switch to speakerphone, another mic is used on most phones. I'm not sure which mic the voice recorder app uses (by bottom mic, do you mean the one used by phone calls?).

The mics kick in based on the phone's situation. If I try to turn mics on/off, the phone tends to go haywire. The OS wants to control the mic based on whether the speakerphone is on or not.

This means the app can't make the app work better.

That being said, I have read a lot about certain cases muffling the mic and also that some people somehow were able to clean the mic hole and it made a big difference.

Sometimes the phones will have a couple mics. They will use two to figure out what is background noise and cancel it out "Noise cancellation". These are the type of settings that sometimes cause the issue that you are experiencing.